I recently published a short article in the Journal of Bioinformatics and Research that investigated host switching in polyomaviruses (which you can also download here).
The analysis was pretty straightforward, although I thought it provided a nice example of how Mauve can help supplement traditional phylogenetic analysis. Also, it looks like most polyomavirus phylogenies in virology journals compare the divergence of individual protein sequences, but I found that analysis of the genomic sequence seems to provide more useful, consistent results.
In the interests of full disclosure, part of the reason I want to plug this paper is that I am on the editorial board for this journal. That said, I do honestly think it is a journal worth considering if you have a paper that isn't a good fit for a more established journal: it is open-access, turn-around time is quick, and it only costs $100 in processing charges for an accepted manuscript.